1.1 - Nucleic Acid Structure and Properties

Question 1

what are the macromolecules of information in the cell?

Answer 1

-DNA
-RNA
-Protein

Question 2

what does DNA, RNA, and protein compromise together?

Answer 2

-the central dogma
-genetic information flow
-DNA goes through replication as well as transcription into RNA
-RNA form is mRNA if synthesizing a protein and this is done through translation (tRNA and rRNA also play a role in protein synthesis)

Question 3

what kind of bond is formed between adenine and thymine?

Answer 3

-double hydrogen bond

Question 4

what kind of bond is formed between cytosine and guanine?

Answer 4

-triple hydrogen bond

Question 5

what is a nucleotide composed of?

Answer 5

-nitrogenous base
-phosphate
-pentose sugar (deoxyribose or ribose)

Question 6

what is a nucleoside composed of?

Answer 6

-pentose sugar (deoxyribose or ribose)
-nitrogenous base

Question 7

what are DNA and RNA considered?

Answer 7

-polynucleotides
-nucleic acids

Question 8

what is the difference in structure between RNA and DNA in terms of their pentose sugars?

Answer 8

-the ribose sugar has an OH on the 2’ carbon
-this is just an H in deoxyribose

Question 9

what connects each of the sugars in DNA and RNA?

Answer 9

-phosphates
-connect the 3’ carbon of one sugar to the 5’ carbon of the adjacent sugar

Question 10

what are the pyrimidine bases?

Answer 10

-cytosine (NH2)
-thymine (H3C)
-uracil (identical to thymine minus the HC3)
-single ring structures

Question 11

what are the purine bases?

Answer 11

-adenine (no double bonded O)
-guanine (double bonded O)
-double ring structures

Question 12

what makes up the backbone of the nucleic acid?

Answer 12

-alternating sugar and phosphate molecules that are linked by phosphodiester bonds between the 5’ and 3’ of two adjacent sugars

Question 13

what is an example of a nucleoside triphosphate in both DNA and RNA?

Answer 13

-adenosine triphosphate (ATP) [RNA]
-deoxyadenosine triphosphate (dATP) [DNA] (type of DNTP)

Question 14

what are the different models for DNA replication that went under consideration?

Answer 14

-conservative model
-semiconservative model
-dispersive model

Question 15

what is the conservative model of DNA replication?

Answer 15

-complementary strands are synthesized from parental “old” templates
-two newly created daughter strands come together and the parent strands also re-associate

Question 16

what is the semi-conservative model of DNA replication?

Answer 16

-each parent strand serves as a template for new daughter DNA strands
-new DNA will contain 1 parent strand and 1 daughter strand

Question 17

what is the dispersive model of DNA replication?

Answer 17

-parent strands are dispersed into 2 new double helices following replication
-each strand consists of old and new DNA
-would involve the cleavage of parent strands during replication

Question 18

how did the meselson stahl experiment disprove conservative replication?

Answer 18

-if conservative replication were true, there would be one light band and one heavy band
-the actual band was an intermediate band, suggesting that all DNA was hybrid

Question 19

how did the meselson stahl experiment disprove dispersive replication?

Answer 19

-if dispersive replication were true, there would be still one band since all DNA would be a hybrid (slowly move up because more light than heavy)
-the actual band after 2 generations would be half light and half hybrid (proving semi conservative)

Question 20

what does a base pair refer to?

Answer 20

-pairing 1 nucleotide in one strand with 1 nucleotide in the complementary strand

Question 21

what is the purpose of hydrogen bonding between the bases in the structure of DNA?

Answer 21

-stabilizes the structure

Question 22

how does DNA form a double helix?

Answer 22

-each base pair rotates 36 degrees relative to the previous base pair
-10 base pairs per turn (3.4nm)
-sugar phosphates form major and minor grooves which are important for DNA/protein interactions
-base pairs that are inside the structure stabilize the helix by base stacking

Question 23

what is a genome?

Answer 23

-all of the genetic material present in an organism (all genes)

Question 24

what genetic element carries essential genes?

Answer 24

-chromosome

Question 25

what are other genetic elements?

Answer 25

-virus genomes, plasmids, organellar genomes (mitochondria), and transposable elements

Question 26

are plasmids found in eukarya?

Answer 26

-not commonly

Question 27

what does packaging of chromosomes in a cell involve?

Answer 27

-supercoiling -double helix is the first level of twist and supercoils are the second level -folding supercoils into loops with DNA binding proteins

Question 28

what controls supercoiling?

Answer 28

-topoisomerases insert or remove them

Question 29

what is negative supercoiling?

Answer 29

-when DNA is twisted about its axis in the opposite sense from the right handed double helix in circular DNA -found in most cells -underwhelmed

Question 30

what is positive supercoiling?

Answer 30

-when DNA is twisted in the same direction -overwhelmed -used in archaea to maintain the DNA in high temp. enviroments

Question 31

what has the sequencing of bacteria and archaea species done for research?

Answer 31

-allowed for bioinformatics to develop as a research field -info can be used to understand nutrient needs of microorganisms -however, just because an organism has a gene, this does not mean that it is expressed (can still learn things and give hints)

Question 32

what can be found from the genetic map of the E.coli K-12?

Answer 32

-1% of its genome encodes tRNAs, rRNAs, and other non-coding RNAs -88% of its genome are protein-encoding genes -rest is not accounted for (regulatory regions or other non-coding regions) -has gal (galactose), trp (tryptophan), his (histidine) operons within

Question 33

what are operons?

Answer 33

-enzyme-encoding genes that function in the same biochemical pathway that are clustered together on the chromosome -have the same promotor -not super common despite their efficiency

Question 34

what influences phenotypes?

Answer 34

-the environment -so not entirely dependent on the genotype

Question 35

what can happen to plasmids through replication?

Answer 35

-gotten rid of because they can be energetically expensive to keep

Question 36

what types of genes can be encoded on a plasmid?

Answer 36

-virulence factors (weapons) -antibiotic resistance -bacteriocins (antimicrobial action on other bacteria) -nitrogen fixation -bioremediation properties

Question 37

what are copy numbers in the context of plasmids?

Answer 37

-can have many copies of a particular plasmid -not just one present